Mercurial > repos > iuc > straindesign_reduce_model
annotate macros.xml @ 0:78b7443af284 draft
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
author | iuc |
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date | Sun, 02 Oct 2022 19:27:33 +0000 |
parents | |
children | 282dd827e28c |
rev | line source |
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0
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
1 <macros> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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2 <!-- GLOBAL --> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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3 <token name="@TOOL_VERSION@">3.1.0</token> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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4 <token name="@VERSION_SUFFIX@">1</token> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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5 <token name="@LICENSE@">MIT</token> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
6 <xml name="requirements"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
7 <requirements> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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8 <requirement type="package" version="@TOOL_VERSION@">straindesign</requirement> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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9 <yield/> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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10 </requirements> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
11 </xml> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
12 <xml name="stdio"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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13 <stdio> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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14 <regex match="WARNING" level="warning" /> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
15 <regex match="ERROR" level="fatal" /> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
16 </stdio> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
17 </xml> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
18 <xml name="citation"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
19 <citations> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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20 <citation type="doi">10.1038/s41467-022-32661-x</citation> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
21 </citations> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
22 </xml> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
23 <xml name="creator"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
24 <creator> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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25 <organization name="BioRetroSynth" url="https://github.com/brsynth"/> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
26 </creator> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
27 </xml> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
28 <xml name="env_variables"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
29 <environment_variables> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
30 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
31 <environment_variable name="USERNAME">\$__user_email__</environment_variable> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
32 </environment_variables> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
33 </xml> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
34 |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
35 <!-- CMDLINE --> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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36 <token name="@CMD_INPUT_MODEL@"><![CDATA[ |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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37 --input-model-file '$model' |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
38 ]]></token> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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39 <token name="@CMD_INPUT_PATHWAY@"><![CDATA[ |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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40 #if $pathway |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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41 --input-pathway-file '$pathway' |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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42 #end if |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
43 ]]></token> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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44 <token name="@CMD_INPUT_MEDIUM@"><![CDATA[ |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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45 #if $medium |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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46 --input-medium-file '$medium' |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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47 #end if |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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48 ]]></token> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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49 <token name="@CMD_BIOMASS_RXN_ID@"><![CDATA[ |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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50 --biomass-rxn-id '$biomass_rxn_id' |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
51 ]]></token> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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52 <token name="@CMD_TARGET_RXN_ID@"><![CDATA[ |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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53 --target-rxn-id '$target_rxn_id' |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
54 ]]></token> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
55 |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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56 <!-- INPUT --> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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57 <xml name="input_model_sbml"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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58 <param name="model" type="data" format="sbml" label="Model" help="SBML input file, model"/> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
59 </xml> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
60 <xml name="input_pathway_sbml"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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61 <param name="pathway" type="data" format="sbml" optional="True" label="Pathway" help="SBML input file, containing heterologous pathway"/> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
62 </xml> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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63 <xml name="input_medium_tsv"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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64 <param name="medium" type="data" format="tabular" optional="True" label="Medium file" help="TSV input file, no header, with three columns: reaction_id, lower_bound, upper_bound"/> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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65 </xml> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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66 <xml name="input_biomass_rxn_id"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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67 <param name="biomass_rxn_id" type="text" value="" label="Biomass reaction ID" help="Reaction ID contains no special characters"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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68 <validator type="empty_field" message="Biomass reaction ID is required"/> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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69 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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70 </param> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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71 </xml> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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72 <xml name="input_target_rxn_id"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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73 <param name="target_rxn_id" type="text" value="" label="Target reaction ID" help="Reaction ID contains no special characters"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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74 <validator type="empty_field" message="Target reaction ID is required"/> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
75 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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76 </param> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
|
77 </xml> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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78 <xml name="input_substrate_rxn_id"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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79 <param name="substrate_rxn_id" type="text" value="" label="Substrate reaction ID" help="Reaction ID contains no special characters"> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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80 <validator type="empty_field" message="Target reaction ID is required"/> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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81 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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82 </param> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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83 </xml> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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84 |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
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85 <!-- HELP --> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
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86 <token name="@HELP_TITLE@"><![CDATA[ |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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87 StrainDesign |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
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88 ============ |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
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89 ]]></token> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
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90 <token name="@HELP_LINK@"><![CDATA[ |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
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91 Project Links |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
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92 ------------- |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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93 |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
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changeset
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94 * `straindesign <https://github.com/brsynth/straindesign>`_ |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff
changeset
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95 * `cameo <https://github.com/biosustain/cameo>`_ |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
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changeset
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96 ]]></token> |
78b7443af284
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
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97 </macros> |